The country's prosecution service meanwhile justified the chaotic situation when authorities first issued an arrest warrant for the Australian whistleblower late on Friday night but then withdrew it the following day.
The Aftonbladet newspaper quoted Assange, 39, as saying he did not know who was "hiding behind" the claims, which came amid a stand-off with Washington over the website's publication of secret Afghan war documents.
Assange said he was shocked by the allegations against him and that he had never had sexual relations with anybody in a way that was not consensual, the tabloid said.
But he said that he had been warned previously that groups such as the Pentagon "could use dirty tricks" to destroy Wikileaks -- adding that he had been particularly warned against being entrapped by sexual scandals.
Assange told Aftonbladet that despite the lifting of the warrant, his enemies would still use the claims to damage Wikileaks, which is set to publish thousands more secret papers about the war in Afghanistan in coming weeks.
He refused to give more details about the two women whose claims sparked the furore, saying that it would impinge on their privacy.
Prosecutors said Saturday that Assange was now "not suspected of rape" and was no longer wanted for questioning on the charge, but added that an investigation into a separate molestation charge remained open.
Assange, Wikileaks website and his aides have strongly denied all the claims.
He had been in Sweden earlier this month giving a press conference on the upcoming release of the last batch of Afghanistan documents, but he generally remains on the move around the world staying with supporters.
The Swedish prosecutor's office issued a statement on Sunday defending its actions.
It said that chief prosecutor Eva Finne, who was responsible for withdrawing the arrest warrant, had "more information available to decide on Saturday than the duty prosecutor on Friday evening."
"A decision regarding restrictive measures, such as this, must always be reevaluated in a preliminary inquiry," the statement added.
The spokeswoman for the prosecutor's office, Karin Rosander, told AFP late Saturday that the procedure followed was normal and would have been launched automatically by the duty prosecutor in serious cases such as rape.
In an interview in the Expressen newspaper, which broke the story, duty prosecutor Maria Häljebo Kjellstrand said that she "did not regret her decision".
The two women who originally made the claims did not make an official complaint and it was the police who took the decision to inform the prosecutors office, she said.
"I received a report from the police which seemed to me to be sufficient to arrest him. On Friday evening I got a call from the police describing what the women said. The information I received was convincing enough for me to take my decision," Häljebo Kjellstrand was quoted as saying.
WikiLeaks has already released nearly 77,000 secret papers about the war against the Taliban and Al-Qaeda in Afghanistan, sparking charges that it had endangered the lives of informants and others named therein.
The website says it had repeatedly asked the Pentagon for help analysing the remaining documents, and Assange has said he wants to avoid publishing the "names of innocent parties that are under reasonable threat".